BioInt  1.02.00
BioInt: An integrative biological object-oriented application framework and interpreter
BioEmblFt Member List
This is the complete list of members for BioEmblFt, including all inherited members.
BioDnaSequence(const string &)BioDnaSequence
BioDnaSequence()BioDnaSequence
BioDnaSequence(const string &seqnam, const string &seq)BioDnaSequence
BioEmblFt()BioEmblFt [inline]
BioEmblFt(const string &de_)BioEmblFt
BioEmblSequence()BioEmblSequence
BioEmblSequence(const string &de_)BioEmblSequence
BioFeatures()BioFeatures [inline]
BioSequence()BioSequence
BioSequence(const string &filename)BioSequence
BioSequence(const string &seqnam, const string &seq)BioSequence
checkDnaSequence()BioDnaSequence
checkSequence()BioSequence
find(const string &words)BioSequence
findPattern(const string &pat)BioSequence
get3PrimeClip(int)BioFeatures
get3PrimeUtr(int)BioFeatures
get5PrimeClip(int)BioFeatures
get5PrimeUtr(int)BioFeatures
get_(int)BioFeatures
get_10Signal(int)BioFeatures
get_35Signal(int)BioFeatures
getAttenuator(int)BioFeatures
getBase(const long &)BioDnaSequence
getCAATSignal(int)BioFeatures
getCds(int)BioFeatures
getComplementarySequence()BioDnaSequence
getComplementarySequence(const long &, const long &)BioDnaSequence
getConflict(int)BioFeatures
getCRegion(int)BioFeatures
getDeletedSequence(const long &, const long &)BioSequence
getDLoop(int)BioFeatures
getDSegment(int)BioFeatures
getEnhancer(int)BioFeatures
getExon(int)BioFeatures
getGap(int)BioFeatures
getGCSignal(int)BioFeatures
getGene(int)BioFeatures
getIDna(int)BioFeatures
getInsertedSequence(const long &, const string &)BioSequence
getIntron(int)BioFeatures
getJSegment(int)BioFeatures
getLtr(int)BioFeatures
getMatPeptide(int)BioFeatures
getMiscBinding(int)BioFeatures
getMiscDifference(int)BioFeatures
getMiscFeature(int)BioFeatures
getMiscRecomb(int)BioFeatures
getMiscRna(int)BioFeatures
getMiscSignal(int)BioFeatures
getMiscStructure(int)BioFeatures
getModifiedBase(int)BioFeatures
getMolecularWeight()BioDnaSequence
getMRna(int)BioFeatures
getmRnaSequence()BioDnaSequence
getmRnaSequence(const long &, const long &)BioDnaSequence
getMutatedSequence(const long &, const char &)BioSequence
getMutatedSequence(const long &, const string &)BioSequence
getMutatedSequence(const char &, const char &)BioSequence
getMutatedSequence(const string &, const string &)BioSequence
getMutatedSequence(const long &, const long &, const string &)BioSequence
getMutatedSequence(string &s1)BioSequence
getNRegion(int)BioFeatures
getNumberOf3PrimeClips()BioFeatures
getNumberOf3PrimeUtrs()BioFeatures
getNumberOf5PrimeClips()BioFeatures
getNumberOf5PrimeUtrs()BioFeatures
getNumberOf_10Signals()BioFeatures
getNumberOf_35Signals()BioFeatures
getNumberOf_s()BioFeatures
getNumberOfAttenuators()BioFeatures
getNumberOfCAATSignals()BioFeatures
getNumberOfCdss()BioFeatures
getNumberOfConflicts()BioFeatures
getNumberOfCRegions()BioFeatures
getNumberOfDLoops()BioFeatures
getNumberOfDSegments()BioFeatures
getNumberOfEnhancers()BioFeatures
getNumberOfExons()BioFeatures
getNumberOfGaps()BioFeatures
getNumberOfGCSignals()BioFeatures
getNumberOfGenes()BioFeatures
getNumberOfIDnas()BioFeatures
getNumberOfIntrons()BioFeatures
getNumberOfJSegments()BioFeatures
getNumberOfLtrs()BioFeatures
getNumberOfMatPeptides()BioFeatures
getNumberOfMiscBindings()BioFeatures
getNumberOfMiscDifferences()BioFeatures
getNumberOfMiscFeatures()BioFeatures
getNumberOfMiscRecombs()BioFeatures
getNumberOfMiscRnas()BioFeatures
getNumberOfMiscSignals()BioFeatures
getNumberOfMiscStructures()BioFeatures
getNumberOfModifiedBases()BioFeatures
getNumberOfMRnas()BioFeatures
getNumberOfNRegions()BioFeatures
getNumberOfOccurrences(const char &ch)BioSequence
getNumberOfOccurrences(const string &pattern)BioSequence
getNumberOfOldSequences()BioFeatures
getNumberOfOperons()BioFeatures
getNumberOfOriTs()BioFeatures
getNumberOfPolyASignals()BioFeatures
getNumberOfPolyASites()BioFeatures
getNumberOfPrecursorRnas()BioFeatures
getNumberOfPrimerBinds()BioFeatures
getNumberOfPrimTranscripts()BioFeatures
getNumberOfPromoters()BioFeatures
getNumberOfProteinBinds()BioFeatures
getNumberOfRbs()BioFeatures
getNumberOfRepeatRegions()BioFeatures
getNumberOfRepeatUnits()BioFeatures
getNumberOfRepOrigins()BioFeatures
getNumberOfRRnas()BioFeatures
getNumberOfSatellites()BioFeatures
getNumberOfSCRnas()BioFeatures
getNumberOfSigPeptides()BioFeatures
getNumberOfSNORnas()BioFeatures
getNumberOfSNRnas()BioFeatures
getNumberOfSources()BioFeatures
getNumberOfSRegions()BioFeatures
getNumberOfSSRs(const string &pat, const int &repeats)BioSequence
getNumberOfStemLoops()BioFeatures
getNumberOfSts()BioFeatures
getNumberOfTATASignals()BioFeatures
getNumberOfTerminators()BioFeatures
getNumberOfTransitPeptides()BioFeatures
getNumberOfTRnas()BioFeatures
getNumberOfUnsures()BioFeatures
getNumberOfVariations()BioFeatures
getNumberOfVRegions()BioFeatures
getNumberOfVSegments()BioFeatures
getOldSequence(int)BioFeatures
getOperon(int)BioFeatures
getOriT(int)BioFeatures
getPercentAT()BioDnaSequence
getPercentGC()BioDnaSequence
getPolyASignal(int)BioFeatures
getPolyASite(int)BioFeatures
getPositionsOfPattern(const string &pat)BioSequence
getPositionsOfSSRs(const string &pat, const int &repeats)BioSequence
getPrecursorRna(int)BioFeatures
getPrimerBind(int)BioFeatures
getPrimTranscript(int)BioFeatures
getPromoter(int)BioFeatures
getProteinBind(int)BioFeatures
getRbs(int)BioFeatures
getRepeatRegion(int)BioFeatures
getRepeatUnit(int)BioFeatures
getRepOrigin(int)BioFeatures
getRRna(int)BioFeatures
getSatellite(int)BioFeatures
getSCRna(int)BioFeatures
getSequence() const BioSequence
getSequenceLength() const BioSequence
getSequenceName() const BioSequence
getSequenceSegment(const long &a, const long &b)BioSequence
getShuffledSequence()BioSequence
getSigPeptide(int)BioFeatures
getSNORna(int)BioFeatures
getSNRna(int)BioFeatures
getSource(int)BioFeatures
getSRegion(int)BioFeatures
getStemLoop(int)BioFeatures
getSts(int)BioFeatures
getTATASignal(int)BioFeatures
getTerminator(int)BioFeatures
getTm()BioDnaSequence
getTransitPeptide(int)BioFeatures
getTranslatedSequence(const int &frameNumber)BioDnaSequence
getTranslatedSequence(const long &, const long &, const int &frameNumber)BioDnaSequence
getTRna(int)BioFeatures
getUnsure(int)BioFeatures
getVariation(int)BioFeatures
getVRegion(int)BioFeatures
getVSegment(int)BioFeatures
readFasta(ifstream &)BioSequence
seqname_BioSequence [protected]
sequence_BioSequence [protected]
setFeatures(vector< string >)BioFeatures
setFt(vector< string > &)BioEmblFt
setSequence(string, vector< string >)BioEmblSequence [protected]
BioDnaSequence::setSequence(const string &seqnam, const string &seq)BioDnaSequence
BioDnaSequence::setSequence(const string &seq)BioDnaSequence
setSequenceName(const string &seqnam)BioDnaSequence
showBioFeatures(ostream &=cout, string st=" ")BioFeatures
showCds(int, ostream &os=cout)BioFeatures
showFeatureKeys(ostream &=cout)BioFeatures
showFeatures(ostream &=cout)BioEmblFt
showInFasta(ostream &=cout)BioSequence
showPositionsOfPattern(const string &pat, ostream &os=cout)BioSequence
showPositionsOfPattern(const string &pat, BioPostScript &ps, const int &xpos=100, const int &ypos=650, const int &w=450, const int &h=20)BioSequence
showSequence(ostream &=cout)BioEmblSequence
showShuffledSequence(ostream &os=cout)BioSequence
showSSRs(const string &pat, const int &repeats, ostream &os=cout)BioSequence
showSSRs(const string &pat, const int &repeats, BioPostScript &ps, const int &xpos=100, const int &ypos=650, const int &w=450, const int &h=20)BioSequence
showTranslatedSequences(ostream &os=cout)BioDnaSequence
showTranslatedSequences(const long &, const long &, ostream &os=cout)BioDnaSequence
showTranslatedSequences(BioHtml &)BioDnaSequence
showTranslatedSequences(BioPostScript &, int startX=75, int startY=200, int len=400)BioDnaSequence
~BioDnaSequence()BioDnaSequence
~BioFeatures()BioFeatures
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